Mapping heterogeneity drivers in human PSC-derived limbal stem cell differentiation through single-cell multi-modal analysis
- 1Radboud University
Abstract
Understanding the molecular underpinnings of stem cell differentiation is pivotal for generating appropriate cell types in cell-based therapies. Differentiation of human pluripotent stem cells (PSC) into corneal limbal stem cells offers a promising avenue to regenerate the corneal epithelium. However, current differentiation strategies remain inconsistent in efficiency and yield heterogeneous cell populations that incompletely recapitulate the regenerative properties of donor-derived limbal stem cells. Here, we mapped the molecular landscape of cell states throughout the differentiation process. First, we construct PSC differentiation paths from single-cell RNA sequencing (scRNA-seq) data using the computational framework of optimal transport, identifying on- and off-track cell states toward the limbal stem cell state. Single cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) was performed to profile accessible genomic regions, and subsequently integrated with scRNA-seq data through gene regulatory network analysis to identify key drivers governing the diverse cell states. We showed that genomic enhancers play a major role in cell state determinations. Through this single-cell multi-modal approach, we identified potential transcription factors driving limbal epithelial lineage specification and off-track cell populations. Our findings provide a framework for rational optimization of PSC-derived limbal stem cell generation to advance the development of corneal cell therapies.
Related
- Directed differentiation with mechanical simulation enhances alveolar-like features in human pluripotent stem cell-derived lung epithelium
- Mapping Projectome Heterogeneity of Subiculum Neuron Cell Types.
- HOTAIR regulates osteogenic–adipogenic differentiation imbalance through the miR-217/DKK1-mediated Wnt/β-catenin pathway in SONFH-BMSCs
- SMURFs regulate mesendoderm differentiation through SMAD2-dependent ubiquitination of CDK9
- Single-cell multimodal analysis reveals enhancer and transcription factor regulatory dynamics during human iPSC-derived cardiomyocyte differentiation
BibTeX
@misc{arts2026mapping,
title = {{Mapping heterogeneity drivers in human PSC-derived limbal stem cell differentiation through single-cell multi-modal analysis}},
author = {J. A. Arts and D. Lima Cunha and S. Harjuntausta and M. Vattulainen and J. G. Smits and I. Bonthuis and D. Fragoso Bento and F. Bocci and H. Skottman and H. Zhou},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.16.751974},
url = {https://www.biorxiv.org/content/10.64898/2026.09.16.751974v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Mapping heterogeneity drivers in human PSC-derived limbal stem cell differentiation through single-cell multi-modal analysis
AU - J. A. Arts
AU - D. Lima Cunha
AU - S. Harjuntausta
AU - M. Vattulainen
AU - J. G. Smits
AU - I. Bonthuis
AU - D. Fragoso Bento
AU - F. Bocci
AU - H. Skottman
AU - H. Zhou
PY - 2026
DA - 2026/09/16
PB - bioRxiv
DO - 10.64898/2026.09.16.751974
UR - https://www.biorxiv.org/content/10.64898/2026.09.16.751974v1
AB - Understanding the molecular underpinnings of stem cell differentiation is pivotal for generating appropriate cell types in cell-based therapies. Differentiation of human pluripotent stem cells (PSC) into corneal limbal stem cells offers a promising avenue to regenerate the corneal epithelium. However, current differentiation strategies remain inconsistent in efficiency and yield heterogeneous cell populations that incompletely recapitulate the regenerative properties of donor-derived limbal stem cells. Here, we mapped the molecular landscape of cell states throughout the differentiation process. First, we construct PSC differentiation paths from single-cell RNA sequencing (scRNA-seq) data using the computational framework of optimal transport, identifying on- and off-track cell states toward the limbal stem cell state. Single cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) was performed to profile accessible genomic regions, and subsequently integrated with scRNA-seq data through gene regulatory network analysis to identify key drivers governing the diverse cell states. We showed that genomic enhancers play a major role in cell state determinations. Through this single-cell multi-modal approach, we identified potential transcription factors driving limbal epithelial lineage specification and off-track cell populations. Our findings provide a framework for rational optimization of PSC-derived limbal stem cell generation to advance the development of corneal cell therapies.
ER -